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AFLAP: assembly-free linkage analysis pipeline using k-mers from genome sequencing data.

  • Author(s): Fletcher, Kyle
  • Zhang, Lin
  • Gil, Juliana
  • Han, Rongkui
  • Cavanaugh, Keri
  • Michelmore, Richard
  • et al.

Our assembly-free linkage analysis pipeline (AFLAP) identifies segregating markers as k-mers in the raw reads without using a reference genome assembly for calling variants and provides genotype tables for the construction of unbiased, high-density genetic maps without a genome assembly. AFLAP is validated and contrasted to a conventional workflow using simulated data. AFLAP is applied to whole genome sequencing and genotype-by-sequencing data of F1, F2, and recombinant inbred populations of two different plant species, producing genetic maps that are concordant with genome assemblies. The AFLAP-based genetic map for Bremia lactucae enables the production of a chromosome-scale genome assembly.

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